Lightroom Folder linking - two folders pointing to the same image.

I have discovered a weird issue with my Lightroom catalog that, unfortunately, resulted in me inadvertently deleting some images. Some folders in the Folders pane are somehow "linked" for the lack of a better term. For example, I have the following two folders:

2006_04_29
2006-04-29

I'm trying to clean up my catalog so I've been moving/renaming (through Lightroom) to fix the issue. The weird thing is if I open an image in 2006_04_29 and look at the system file info, it shows it actually lives in 2006-04-29. Unfortunately, this is after I deleted a dozen or so folders. Deleting from either folder deletes from both. I'm surprised the catalog optimization or synchronization both didn't fix it.